PHLDA2 (Pleckstrin homology-like domain, family A, member 2)

2020-10-01   Renan Gomes do Nascimento , Flavia Rotea Mangone Ana Carolina Pavanelli , Maria Aparecida Nagai 

Identity

HGNC
LOCATION
11p15.4
LOCUSID
ALIAS
BRW1C,BWR1C,HLDA2,IPL,TSSC3

Abstract

Review of the PHLDA2 gene, with data on DNA, the protein encoded by this gene, and biological and pathological implications.

DNA/RNA

Description

DNA size: 1,148 kb, 2 exons.

Transcription

mRNA size 920 pb NM_003311.4. Only one transcript variant encoding PHLDA2 have been described. NM_003311 - Homo sapiens pleckstrin homology-like domain, family A, member 2 (PHLDA2), mRNA -> Transcript size: 920 bp. NP_003302.1. (https://www.ncbi.nlm.nih.gov/nuccore/NM_003311; http://www.ensembl.org/id/ENST00000314222.5).

Proteins

Atlas Image
Figure 1. Schematic representation of the modular structure of the PHLDA2 protein. The PHLDA2 protein structure consists of a single PHL domain (pleckstrin homology-like) from amino acid residues 7 to 99, flanked by short terminal extensions.

Description

The protein encoded by the PHLDA2 gene consists of 152 amino acids, a molecular weight of 17.1 kDa, composed mainly of the PHL domain (93aa) (Frank et al., 1999). The PHL domain present in its structure has a moderate binding affinity to phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol 3,4,5-triphosphate (PIP3) (Frank et al., 2002; Saxena et al., 2002). NP_003302.1 (https://www.ncbi.nlm.nih.gov/protein/NP_003302)

Expression

According to the integrative human mRNA and protein expression map, the PHLDA2 is remarkably expressed in placental tissue. Tissues of stomach, colon, prostate, duodenum, small intestine, and kidney are those of more abundant expression (Fagerberg et al., 2013). A monoallelic expression is observed in human fetal tissues such as the kidney, intestine, liver, heart, being the maternal allele preferentially expressed (Lee & Feinberg, 1998). It has been shown that PHLDA2 expression is down-regulated under hypoxia in human trophoblasts (Roh et al., 2005). PHLDA2 has been described as the first apoptotic related gene regulated by genomic imprinting (Lee & Feinberg, 1998). PHLDA2 expression is negatively regulated at the minimum by two different mechanisms, one by at least to miRNAs ( MIR214 MIR148A-5p) and by a methyltransferase called EZH2 (Lv et al., 2015; Idishi et al., 2018; Li et al., 2019).

Localisation

The mature PHLDA2 protein subcellular localization is at the cytoplasm, cellular membrane, and also peripheral membrane protein (https://www.uniprot.org/uniprot/Q53GA4).

Function

The PHLDA2 gene is one of several genes clustered at 11p15.5 domain, an important region for tumor suppressor genes. Changes in this chromosomal region have already been described in Beckwith-Wiedemann syndrome, hydatidiform mole, and different types of tumors (Hu et al., 1997, Weksberg et al., 2005, Feinberg, 1999).
The protein encoded by the PHLDA2 gene can play different biological roles depending on cell or tissue specificity (https://www.uniprot.org/uniprot/Q53GA4). In mouse models, PHLDA2 negatively controls glycogen storage during pregnancy, negatively regulates the expression of a variety of placental hormones through the spongiotrophoblast layer (Tunster et al., 2010; Tunster et al., 2016).
PHLDA2 (TSSC3) has been shown to induce apoptosis by increasing the intrinsic pro-apoptotic pathway members such as BAK1, BCL2L11 (BIM), CYCS (Cyt c), and the BAX: BCL2 ratio and downregulating anti-apoptotic proteins like BCL2 and FAS in human osteosarcoma cell lines (Dai et al., 2012; Huang et al., 2012). PHLDA2 has also been shown to have a role in anoikis resistance and metastasis through the interaction with RANBP9 and downregulation of the SRC -dependent Akt pathway in osteosarcoma cells (Dai et al., 2016).
Experimental evidence also associated increased expression of PHLDA2 in trophoblast cells with cell-cycle inhibition through the reduction of cyclin D1 and cyclin E ( CCND1 and CCNE1) arresting cells in G0/G1 phase of the cell cycle (Jin et al., 2015).
PHLDA2 increases epithelial-mesenchymal transition (EMT) of osteosarcoma cells by upregulating mesenchymal markers, such as CDH2 (N-cadherin), VIM (Vimentin), and SNAI1 (SNAIL), and inhibiting the epithelial markers like CDH1 (E-cadherin) (Dai et al., 2016, Lv et al., 2016). Additionally, PHLDA2 can inhibit Src/Akt pathway suppressing self-renewal in osteosarcoma stem cells (Yan et al., 2017), and this Src/Akt pathway inactivation prevents MTOR phosphorylation, that drives osteosarcoma cells to autophagy, contributing to the inhibition of tumorigenesis and metastasis (Zhao et al., 2018).
Atlas Image
Figure 2 - Schematic diagram of the modulators, effectors, and biological processes associated with PHLDA2 expression. Different stimuli can modulate PHLDA2 expression. Therefore, various biological processes are associated depending on the stimulus and cellular effectors.

Homology

The human protein encoded by the PHLDA2 gene is highly conserved in vertebrates. Orthologs have been described in Pan troglodytes (chimpanzee); Macaca mulatta (Rhesus monkey); Bos taurus (cattle); Mus musculus (house mouse); Rattus norvegicus (Norway rat); Gallus gallus (chicken), Xenopus tropicalis (tropical clawed frog), Danio rerio (zebrafish) (https://www.ncbi.nlm.nih.gov/homologene/2482), among others also described at Ensembl genome browser (https://www.ensembl.org/ PHLDA2 ENSG00000181649, Ensembl release 100 - April 2020). Moreover, two protein paralogues are known: PHLDA1 (pleckstrin homology like domain, family A, member 1) e PHLDA3 (pleckstrin homology like domain, family A, member 3) (https://www.ensembl.org/ PHLDA2 ENSG00000181649)

Implicated in

Top note
The PHLDA2 gene is located in a chromosomal region considered an important center for imprinting and localizing tumor suppressor genes. Alterations in the expression of PHLDA2 has been reported in different types of tumors. However, the attribution of its oncogenic or suppressive functions in tumor development is under investigation (Dai et al., 2012; Hsu et al., 2017; Zhao et al., 2018).
Entity name
Placental and Fetal Development
Note
Several reports in the literature have been shown the role played by PHLDA2 expression in placental development. Salas et al. (2004), using a transgenic model, demonstrated that loss of Phlda2 expression in animals with wild background causes placentomegaly and increased expression of this gene in the placenta causes a significant delay in placental growth. High expression of the PHLDA2 leads to decreased expression of genes associated with lipids production, regulated by spongiophoblasts, causing placental dwarfism and reduction in the accumulation of placental glycogen (Tunster et al., 2016). High expression of PHLDA2 was also significantly associated with decreased birth weight, showing that PHLDA2 can act to decrease body weight by reducing the size and function of the placenta (Apostolidou et al., 2007). The expression of PHLDA2 in the placenta was significantly correlated with decreased femur growth in fetuses between 19 and 34 weeks of gestation and later associated with a lower bone mineral content of the child at the age of four (Lewis et al., 2012).
PHLDA2 expression has been associated with hydatidiform mole disease, in which an increase in PHLDA2 expression was observed in trophoblast cells, possibly due to trisomy of the 11p15.5 chromosomal region (Fisher et al., 2004).
PHLDA2 expression has also been associated with the development of spontaneous abortions, where the increased expression of this gene was observed in placental and fetal samples in the first half of the interrupted pregnancy, showing that this gene may be a possible marker in fetal growth. In vitro studies, with trophoblast cells with overexpression of PHLDA2, showed inhibition of cell growth, migration, and invasion. On the other hand, PHLDA2 reduced expression showed the opposite effect, with an increase in migration and invasion, suggesting the involvement of PHLDA2 in the development of pre-eclampsia due to inhibition of proliferation, migration, and invasion of trophoblastic cells (Jin et al., 2015).
Entity name
Lung cancer
Note
High expression of PHLDA2 was observed in samples of lung adenocarcinoma compared to adjacent normal tissue. Increased PHLDA2 expression was associated with poor patient survival, suggesting an oncogenic role of PHLDA2 in the development of lung cancer (Hsu e al., 2017). PHLDA2 was also identified as negatively regulated in lung cancer cell lines after inhibiting the EGFR/ ERBB2 pathway. In addition, PHLDA2 expression showed a direct correlation with the expression of p-AKT, suggesting that PHLDA2 may act in the regulation of oncogenic signaling pathways (Wang et al., 2018).
Entity name
Osteosarcoma
Note
In osteosarcomas, PHLDA2 has been investigated and reported as a possible gene with tumor-suppressive activities. Osteosarcoma samples showed reduced expression of PHLDA2 when compared to adjacent normal tissue and were found to be associated with clinical-pathological data, such as high tumor grade, presence of metastasis, and tumor recurrence (Dai et al., 2012; Wang et al., 2016). PHLDA2 knockdown results in increased cell proliferation and colony formation decreased cell division and apoptosis, and increased tumor growth, which suggests that inactivation of the PHLDA2 protein may contribute to the development and progression of these tumors (Dai et al., 2012). Osteosarcoma cells with PHLDA2 overexpression show increased autophagy and reduced MTOR phosphorylation via SRC/AKT, leading to suppression of tumorigenesis and metastatic phenotype (Zhao et al., 2018). Recently, negative regulation of PHLDA2 expression has been associated with MIR214 expression, promoting resistance to radiotherapy, pulmonary metastasis, and activation of the AKT pathway, suggesting that PHLDA2/AKT may be a new radiotherapy target in osteosarcomas (Yi Li, et al. 2019).
Entity name
Pancreatic adenocarcinoma
Note
Pancreatic adenocarcinoma is one of the most lethal cancers, in which only 5% of patients have recurrence-free survival in 5 years. Low expression of PHLDA2, directly modulated by MIR148A-5p, inhibits proliferation, migration, and invasion and increases apoptosis in PANC-1 cells, which are derived from pancreatic carcinoma (Idich et al., 2018).
Entity name
Colorectal cancer
Note
A recent study found that colorectal tumors showed higher expression of PHLDA2 (transcripts and proteins) when compared to adjacent normal tissues. The inactivation of these proteins in colorectal cancer-derived lineage promoted inhibition of cell growth, migration and invasion, and reduced expression of proteins related to the epithelium-mesenchymal transition, and induction of autophagy through the PI3K/AKT signaling pathway, suggesting that PHLDA2 may play a role in the development and progression of colorectal cancer (Zhan Ma et al., 2020).
Entity name
Breast cancer
Note
There are few studies in the literature addressing the expression of PHLDA2 in breast cancer. Moon et al. (2015), using patient-derived xenograft (PDX) technique, sought to investigate the prognostic role and a gene signature in breast tumors of the triple-negative subtype. PHLDA2 was shown to be positively regulated in cells of the triple negative breast cancer subtype, and its silencing led to a reduction in invasion and proliferation of MDA-MB-231 cells, suggesting the involvement of PHLDA2 in the breast cancer.

Bibliography

Pubmed IDLast YearTitleAuthors
203798902010Identification of differentially expressed genes associated with osteochondrosis in standardbred horses using RNA arbitrarily primed PCR.Austbø L et al
269315682016Tousled-like kinase 2 regulates recovery from a DNA damage-induced G2 arrest.Bruinsma W et al
225888772012The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.Cerami E et al
161433982006Gene profiling involved in immature CD4+ T lymphocyte responsible for systemic lupus erythematosus.Deng YJ et al
111727072001Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1.Emili A et al
235502102013Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.Gao J et al
272747262016A Cross-Study Biomarker Signature of Human Bronchial Epithelial Cells Infected with Respiratory Syncytial Virus.Gardinassi LG et al
126601732003Human Tousled like kinases are targeted by an ATM- and Chk1-dependent DNA damage checkpoint.Groth A et al
239113192013Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network.Gulsuner S et al
255149262015PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.Hornbeck PV et al
113316022001Asf1 links Rad53 to control of chromatin assembly.Hu F et al
194546172009Genetic variation in the chromosome 17q23 amplicon and breast cancer risk.Kelemen LE et al
274893602016Amplification of TLK2 Induces Genomic Instability via Impairing the G2-M Checkpoint.Kim JA et al
276948282016Comprehensive functional analysis of the tousled-like kinase 2 frequently amplified in aggressive luminal breast cancers.Kim JA et al
264864552015Exploratory biomarker analysis for treatment response in KRAS wild type metastatic colorectal cancer patients who received cetuximab plus irinotecan.Kim ST et al
245988212014Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication.Klimovskaia IM et al
129550712003Suppression of Tousled-like kinase activity after DNA damage or replication block requires ATM, NBS1 and Chk1.Krause DR et al
222919052012GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival.Lee CH et al
301011942018Tousled-like kinases stabilize replication forks and show synthetic lethality with checkpoint and PARP inhibitors.Lee SB et al
274798432016Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability.Lelieveld SH et al
307607332019Inactive Tlk associating with Tak1 increases p38 MAPK activity to prolong the G2 phase.Liaw GJ et al
302078342019TLK2 enhances aggressive phenotypes of glioblastoma cells through the activation of SRC signaling pathway.Lin M et al
272512752016Proteogenomics connects somatic mutations to signalling in breast cancer.Mertins P et al
299550622018Molecular basis of Tousled-Like Kinase 2 activation.Mortuza GB et al
215724172011Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.O'Roak BJ et al
200167862009Phosphorylation-mediated control of histone chaperone ASF1 levels by Tousled-like kinases.Pilyugin M et al
298611082018De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder.Reijnders MRF et al
309231722019Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders.Schluth-Bolard C et al
287081362017Differential requirements for Tousled-like kinases 1 and 2 in mammalian development.Segura-Bayona S et al
114704142001Identification of human Asf1 chromatin assembly factors as substrates of Tousled-like kinases.Silljé HH et al
216075842011Evaluation of associations between common variation in mitotic regulatory pathways and risk of overall and high grade breast cancer.Stevens KN et al
126007202003Abeta42 generation is toxic to endothelial cells and inhibits eNOS function through an Akt/GSK-3beta signaling-dependent mechanism.Suhara T et al
315588422020Severe neurodevelopmental disease caused by a homozygous TLK2 variant.Töpf A et al
293467702018Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder.Takata A et al
200547282010Genetic regulatory network analysis for app based on genetical genomics approach.Wang X et al
94275651997cDNA cloning and chromosomal mapping of genes encoding novel protein kinases termed PKU-alpha and PKU-beta, which have nuclear localization signal.Yamakawa A et al
104551591999Nuclear localization of protein kinase U-alpha is regulated by 14-3-3.Zhang S et al

Other Information

Locus ID:

NCBI: 7262
MIM: 602131
HGNC: 12385
Ensembl: ENSG00000181649

Variants:

dbSNP: 7262
ClinVar: 7262
TCGA: ENSG00000181649
COSMIC: PHLDA2

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000181649ENST00000314222Q53GA4

Expression (GTEx)

0
5
10
15
20
25
30
35
40

References

Pubmed IDYearTitleCitations
202019242010Genome-wide association study of alcohol dependence implicates a region on chromosome 11.159
215555182011The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.60
171803442007Elevated placental expression of the imprinted PHLDA2 gene is associated with low birth weight.55
93284651997The IPL gene on chromosome 11p15.5 is imprinted in humans and mice and is similar to TDAG51, implicated in Fas expression and apoptosis.43
300927892018TSSC3 promotes autophagy via inactivating the Src-mediated PI3K/Akt/mTOR pathway to suppress tumorigenesis and metastasis in osteosarcoma, and predicts a favorable prognosis.19
204849772010Gene expression pattern of IGF2, PHLDA2, PEG10 and CDKN1C imprinted genes in spontaneous miscarriages or fetal deaths.17
224446682012Maternal inheritance of a promoter variant in the imprinted PHLDA2 gene significantly increases birth weight.17
268454472016Downregulation of tumor suppressing STF cDNA 3 promotes epithelial-mesenchymal transition and tumor metastasis of osteosarcoma by the Wnt/GSK-3β/β-catenin/Snail signaling pathway.17
220219092012TSSC3 overexpression associates with growth inhibition, apoptosis induction and enhances chemotherapeutic effects in human osteosarcoma.15
226104812012TSSC3 overexpression reduces stemness and induces apoptosis of osteosarcoma tumor-initiating cells.15

Citation

Renan Gomes do Nascimento ; Flavia Rotea Mangone Ana Carolina Pavanelli ; Maria Aparecida Nagai

PHLDA2 (Pleckstrin homology-like domain, family A, member 2)

Atlas Genet Cytogenet Oncol Haematol. 2020-10-01

Online version: http://atlasgeneticsoncology.org/gene/41708/phlda2